Man pages for BIGDAWG
Case-Control Analysis of Multi-Allelic Loci

AAmino Acid Analysis Function
AA.df.checkContingency Table Check
AAtable.builderAmino Acid Contingency Table Build
AlignmentFilterAlignment Filter
AlignObj.CreateAlignment Object Creator
AlignObj.UpdateUpdated Alignment Object Creator
A.wrapperAmino Acid Wrapper
BIGDAWGBIGDAWG Main Wrapper Function
buildHAPnamesHaplotype Name Builder
buildHAPsetsHaplotype List Builder
cciCase-Control Odds ratio calculation and graphing
cci.pvalCase Control Odds Ratio Calculation from Epicalc
cci.pval.listCase Control Odds Ratio Calculation from Epicalc list...
CheckAllelesAllele Legitimacy Check
Check.CoresCheck Cores Parameters
CheckHLAHLA Formatting Check
CheckLociLoci Legitimacy Check
Check.ParamsCheck Input Parameters
CheckReleaseFunction to Check Release Versions
DRB345.flagDRB345 haplotype zygosity flag check
DRB345.parserDRB345 Column Processing
DRB345.zygosityDRB345 haplotype zygosity checker
Err.LogError Code Display and Logging
EVSremovalExpression Variant Suffix Removal
ExonPtnAlign.CreateProtein Exon Alignment Formatter
ExonPtnListExon 2 (class II) or 2/3 (class I) protein alignments.
FixAlleleNameAllele Name Format Fix
getAllele.CountRecompute number of alleles
getCS.MatChi square matrices
getCS.statChi square test statistic
GetFieldHLA trimming function
GetFilesFile Fetcher
getHapHaplotype Table Maker
getObsFreqObserved Frequency
HLA_dataExample HLA Dataset
H.MCHaplotype Analysis Function for Multicore
H.MC.wrapperHaplotype Wrapper for Multicore
HWEHardy Weinbergy Equilibrium Function
HWE.ChiSqHardy Weinbergy Equilibrium Function
HWE.wrapperHardy-Weinbery Wrapper
LLocus Analysis Function
L.wrapperLocus Wrapper
make2x2Creation of a 2x2 table using the indicated orientation.
makeCombGenotype Combination Maker
MergeData_OutputData Object Merge and Output
PgrpExtractHLA P group Finder
PgrpFormatHLA P group File Formatter
PreCheckData Summary Function
rmABstringsReplace absent allele strings
RunChiSqChi-squared Contingency Table Test
summaryGeno.2Haplotype missing Allele summary function
TableMakerTable Maker
UpdateReleaseUpdate function for protein aligment upon new IMGT HLA data...
BIGDAWG documentation built on Sept. 6, 2017, 9:03 a.m.